Software used during the course
VM setup guide can be found here: NGS Virtualbox Setup Guide
This table summarizes all installed software, their versions, official download links, and commands to verify installation.
| Software | Version | Download Link | Test Command | Dependencies |
|---|---|---|---|---|
| Samtools | 1.15.1 | Link | samtools --version |
None |
| Bcftools | 1.15.1 | Link | bcftools --version |
None |
| Bedtools | 2.30.0 | Link | bedtools --version |
None |
| OpenMPI | 4.1.4 | Link | mpirun --version |
None |
| R-base | 4.0.5 | Link | R --version |
None |
| Bowtie2 | 2.4.5 | Link | bowtie2 --version |
None |
| MACS2 | 2.2.7.1 | Link | macs2 --version |
Python, NumPy |
| MEME Suite | 5.4.1 | Link | meme --version |
Perl |
| UCSC BedGraphToBigWig | 377 | Link | ucsc-bedgraphtobigwig |
None |
| UCSC FetchChromSizes | 377 | Link | ucsc-fetchchromsizes |
None |
| R-sleuth | 0.30.0 | Link | R -e 'library(sleuth)' |
R, Bioconductor |
| Bioconductor-rhdf5 | 2.34.0 | Link | R -e 'library(rhdf5)' |
R, HDF5 |
| Bioconductor-rhdf5filters | 1.2.0 | Link | R -e 'library(rhdf5filters)' |
R, HDF5 |
| Bioconductor-rhdf5lib | 1.12.0 | Link | R -e 'library(rhdf5lib)' |
R, HDF5 |
| HDF5 | 1.10.5 | Link | h5cc -showconfig |
None |
| Hisat2 | 2.2.1 | Link | hisat2 --version |
None |
| Kallisto | 0.46.2 | Link | kallisto version |
None |
| BWA | 0.7.17 | Link | bwa |
None |
| Assembly-Stats | 1.0.1 | Link | assembly-stats |
None |
| Canu | 2.2 | Link | canu --version |
Java, gnuplot |
| Kmer-Jellyfish | 2.3.0 | Link | jellyfish --version |
None |
| Seqtk | 1.3 | Link | seqtk |
None |
| Velvet | 1.2.10 | Link | velveth --help |
None |
| Wtdbg | 2.5 | Link | wtdbg2 |
None |
| GenomeScope2 | 2.0 | Link | N/A | R, Bioconductor |
| FreeBayes | 0.9.21.7 | Link | freebayes --version |
None |
| GATK4 | 4.2.6.1 | Link | gatk --version |
Java |
| Picard | 2.27.4 | Link | picard -h |
Java |
| Minimap2 | 2.24 | Link | minimap2 --version |
None |
| Sniffles | 2.0.7 | Link | sniffles -h |
None |
| Dysgu | latest | Link | dysgu --version |
Python, scikit-learn |
| Breakdancer | 1.4.5 | Link | breakdancer-max -h |
Perl, Samtools |
| IGV | 2.14.1 | Link | igv |
Java |
| Jupyter Notebook | 1.0.0 | Link | jupyter --version |
Python, IPython |
| LaTeX (for Jupyter) | latest | Link | pdflatex --version |
None |
Bioinformatics Environments and Installed Software
| Environment Name | Software | Version |
|---|---|---|
| ngsbio | Samtools | 1.15.1 |
| Bcftools | 1.15.1 | |
| Bedtools | 2.30.0 | |
| OpenMPI | 4.1.4 | |
| R-base | 4.0.5 | |
| Bowtie2 | 2.4.5 | |
| MACS2 | 2.2.7.1 | |
| MEME Suite | 5.4.1 | |
| UCSC BedGraphToBigWig | 377 | |
| UCSC FetchChromSizes | 377 | |
| R-sleuth | 0.30.0 | |
| Bioconductor-rhdf5 | 2.34.0 | |
| Bioconductor-rhdf5filters | 1.2.0 | |
| Bioconductor-rhdf5lib | 1.12.0 | |
| HDF5 | 1.10.5 | |
| Hisat2 | 2.2.1 | |
| Kallisto | 0.46.2 | |
| BWA | 0.7.17 | |
| Assembly-Stats | 1.0.1 | |
| Canu | 2.2 | |
| Kmer-Jellyfish | 2.3.0 | |
| Seqtk | 1.3 | |
| Velvet | 1.2.10 | |
| Wtdbg | 2.5 | |
| GenomeScope2 | 2.0 | |
| FreeBayes | 0.9.21.7 | |
| GATK4 | 4.2.6.1 | |
| Picard | 2.27.4 | |
| Minimap2 | 2.24 | |
| Sniffles | 2.0.7 | |
| Dysgu | latest | |
| Breakdancer | 1.4.5 | |
| chipseq-project | R-ngsplot | latest |
| Python | 2.7 | |
| jupyter | Jupyter Notebook | 1.0.0 |
| Pandoc | 2.12 | |
| system-wide | IGV | 2.14.1 |
| LaTeX | latest |
- ngsbio: The primary bioinformatics environment containing sequencing analysis tools.
- chipseq-project: Contains tools specific to ChIP-seq analysis.
- jupyter: Environment for running Jupyter Notebooks.
- system-wide: Software installed outside Conda (e.g., IGV, LaTeX).
For installation and setup, please refer to the following guides:
- Oracle VM VirtualBox Installation Guide – Detailed instructions for installing and configuring VirtualBox on different operating systems. (Note: Separate installations are needed for Intel-based and ARM-based Macs, and the VDI files will differ.)
The Host Operating System Requirements are:
- RAM requirement: 8GB (preferably 12GB)
- Processor requirement: 4 processors (preferably 8)
- Hard disk space: 200GB
- Admin rights to the computer
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
Each course landing page is assigned a DOI via Zenodo, providing a stable and citable reference. These DOIs can be found on the respective course landing pages and can be included in CVs or research publications, offering a professional record of the course contributions.
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